Microbiome digest, December 8, 2014

Bioinformatic tools for tree building and metagenomics, microbiome of iPads in hospitals, and stool samples from indigenous cultures.
Human clinical microbiome

MetaGeniE: Characterizing Human Clinical Samples Using Deep Metagenomic Sequencing – Arun Rawat – PLOS ONE

“We have developed an efficient strategy that identifies “all against all” relationships between sequencing reads and reference genomes.”

Human gut microbiome

Human Fecal Microbiome–Based Biomarkers for Colorectal Cancer – Vilvapathy Narayanan – Cancer Prevention Research

“A recent study by Zackular and colleagues… provides an important way forward here in showing that specific analysis of multiple aspects of the microbiome composition in toto provides reliable detection of both precancerous and cancerous lesions. “

Plant microbiome

Covalently linked hopanoid-lipid A improves outer-membrane resistance of a Bradyrhizobium symbiont of legumes – Alba Silipo – Nature Communications

“Here we demonstrate that a photosynthetic Bradyrhizobium strain, symbiont of Aeschynomene legumes, synthesizes a unique LPS bearing a hopanoid covalently attached to lipid A.”

Microbiome of the built environment

* Surface Microbiology of the iPad Tablet Computer and the Potential to Serve as a Fomite in Both Inpatient Practice Settings as Well as Outside of the Hospital Environment – Elizabeth B. Hirsch – PLOS ONE

“Thirty iPads belonging to faculty with a variety of practice settings were sampled to determine the presence and quantity of clinically-relevant organisms.”

Bioinformatic tools

A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation – Kalliopi Trachana – PLOS ONE

“Therefore, we constructed high quality “gold standard” orthologous groups that can serve as a benchmark set for orthology inference in bacterial species.”

Towards more accurate ancestral protein genotype–phenotype reconstructions with the use of species tree-aware gene trees – Mathieu Groussin – Molecular Biology and Evolution

“Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer and loss (DTL) of genes statistically increases ASR accuracy.”

IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies – Lam-Tung Nguyen – Molecular Biology and Evolution

“We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented.”

Sampling and DNA extraction techniques

Nasal Screening for MRSA: Different Swabs – Different Results! – Philipp Warnke – PLOS ONE

“This study investigates the performance of different swab-types in nasal MRSA-screening by utilizing a unique artificial nose model to provide realistic and standardized screening conditions.”

Microbes in the news

Les Dethlefsen from our lab did an excellent “AMA” (ask me anything) on Reddit/Science today, on the human gut microbiota. Read the questions and Les’ answers here.

* Fecal Matters: A Stepping Stool to Understanding Indigenous Cultures – Daniella Lowenberg – PLOS Blogs

“Suspecting that this excrement is rich in biological clues, a group of researchers conducted experiments to investigate fecal microbiomes and published a study in PLOS ONE detailing insights into the diets and lifestyles of two ancient indigenous cultures of Puerto Rico”

Quantifying the Microbiome and the State of Crowd Science with Jessica Richman (1h Podcast) – The Quantified Body

“…we have an excellent guest today to bring us up to date on all this. Jessica Richman, is CEO and co-founder of uBiome.”

* If you think your city subway only consists of smelly disgruntled commuters, think again… – Marcus Leung – MicroBEnet

“Have you ever wondered what microbes are around you when you take public transport? Personally, I think about it every day during my two-hour subway commute to and from our lab here in Hong Kong.”

Science, publishing, and career

Metascience could rescue the ‘replication crisis’ – Jonathan W. Schooler – Nature

“Metascience, the science of science, uses rigorous methods to examine how scientific practices influence the validity of scientific conclusions. “

Interactive notebooks: Sharing the code – Helen Shen – Nature

“The free IPython notebook makes data analysis easier to record, understand and reproduce.”

Column: It takes time and a team to win grants – Ingrid Eisenstadter – Nature

“All our applicants are people who were bright enough to get PhDs and MDs, but the proposals we receive tend to share the same flaws, whether they come from recent graduates or from researchers with years of experience.”

Elsevier bad for your h-index? – Ferniglab

“The negotiations between the Dutch universities and Elsevier have foundered…., which means that from 1 January 2015, Dutch researchers will no longer have access to Elsevier journals.”

Sexy molecules! Comedian Megan Amram talks ‘Science… for Her!’ (Q&A) – Amanda Kooser -CNET

“”Parks and Recreation” writer Megan Amram offers up a “raunchy, crazy” textbook full of carbon dating, physics as nail art and kale.”

Bik’s Picks

YouTube video: Brian Cox visits the world’s biggest vacuum chamber – Human Universe: Episode 4 Preview – BBC Two

“…what happens when a bowling ball and a feather are dropped together under the conditions of outer space (vacuum – EB).”

Study in paradise: Stanford professors turn Hawaii into a living science classroom – Bjorn Carey – Stanford News

“Students in the School of Earth Science’s Wrigley Field Program in Hawaii spend the quarter measuring vegetation, coral reefs and volcanoes to understand the dynamics of one of the planet’s most interesting ecosystems.”

[hr]

Non-human microbiome digest, October 28, 2014

Posted on October 28, 2014 by eliesbik

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.”

[hr]

Microbiome digest, October 13, 2014

Posted on October 13, 2014 by eliesbik

Preterm infant gut microbiome, fecal transplants, microbes in space, and microbiome of 8 different fish species.

Pregnancy and birth

* Development of the preterm infant gut microbiome: a research priority – Maureen W Groer (Jack Gilbert lab) – Microbiome

“This review provides a synthesis of our understanding of the normal development of the infant gut microbiome and contrasts this with dysbiotic development in the VLBW infant.”

Fluorescence in situ hybridization for identification of microorganisms in acute chorioamnionitis – D. Schmiedel – Clinical Microbiology and Infection

“Using a diagnostic fluorescence in situ hybridization probe panel, we visualized Staphylococcus aureus and Streptococcus mitis group in two cases of acute chorioamnionitis. “

The Role of Mycoplasma and Ureaplasma in Adverse Pregnancy Outcomes – Amy P. Murtha – Obstetrics and Gynecology Clinics of North America

* Impact Of Lifestyle On The Gut Microbiota Of Healthy Infants And Their Mothers – The Aladdin Birth Cohort – Helena Marell Hesla – FEMS Microbiology Ecology

“Samples collected from infants at ages six days, three weeks, two months and six months and from their mothers before and after delivery, respectively, were analyzed using 454-pyrosequencing.”

Human gut microbiome

* Oral, Capsulized, Frozen Fecal Microbiota Transplantation for Relapsing Clostridium difficile Infection – Ilan Youngster – JAMA

“Self-ranked health scores improved significantly on a scale of 1 to 10 from a median of 5 for overall health and 4.5 for gastrointestinal-specific health on the day prior to FMT to 8 after FMT administration for both overall and gastrointestinal health (P = .001).”

* Impact of Experimental Hookworm Infection on the Human Gut Microbiota – Cinzia Cantacessi – Journal of Infectious Diseases

“We used 16S rRNA gene amplification and pyrosequencing to characterize, for the first time to our knowledge, the differences in composition and relative abundance of fecal microbial communities in human subjects prior to and following experimental infection with the blood-feeding intestinal hookworm, Necator americanus. “

Genomics of schizophrenia: time to consider the gut microbiome? – T G Dinan – Molecular Psychiatry

“To date, this vast quantity of DNA has been largely ignored in schizophrenia research.”

Animal microbiome

Comparative study on gastrointestinal microbiota of eight fish species with different feeding habits – Jinjin Li – Journal of Applied Microbiology

“The V1 to V3 regions of 16S rRNA gene were analyzed by highthroughput sequencing (454 platform) to compare the gut microbiota of different fish species. “

Dining local: the microbial diet of a snail that grazes microbial communities is geographically structured – Richard O’Rorke – Environmental Microbiology

“we collected 102 snail fecal samples as a proxy for diet, and 102 matched-leaf samples from four locations. We used Illumina amplicon sequencing to determine bacterial and fungal community composition. “

Bacterial associates of seed-parasitic wasps (Hymenoptera: Megastigmus) – Amber R Paulson – BMC Microbiology

“We characterized the bacterial symbionts of Megastigmus (Hymenoptera: Torymidae), a lineage of seed-parasitic chalcid wasps, with the goal of identifying microbes that might play an important role in aiding development within seeds, including supplementing insect nutrition or manipulating host trees.“

Bioreactor microbiome

Biofouling and Microbial Communities in Membrane Distillation and Reverse Osmosis – Katherine R. Zodrow – Environmental Science & Technology

“Phylogenetic analysis using next-generation sequencing of 16S ribosomal DNA showed significant shifts in the microbial communities. “

Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture – Amy A Boaro – FEMS Microbiology Ecology

“16S rDNA pyrosequencing results revealed increased alpha diversity in the microbial community after the perturbation, and a persistence of the dominant community members over the duration of the experiment.”

Environmental microbiome

Effects of Bioavailable Heavy Metal Species, Arsenic, and Acid Drainage from Mine Tailings on a Microbial Community Sampled Along a Pollution Gradient in a Freshwater Ecosystem – Togwell A. Jackson – Geomicrobiology Journal

“Ribosomal ribonucleic acid, fatty acid, and phospholipid analyses, along with assays of CO2 production, denitrification, and enzyme activities, were performed to characterise the microflora; and environmental conditions were defined by various physicochemical analyses, including determination of bioavailable metal species. “

The role of macrobiota in structuring microbial communities along rocky shores – Catherine A Pfister, Jack A Gilbert, Sean M Gibbons – PeerJ

“At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton.”

Microbes in (simulated) space

The development and succession of microbial communities in 90-day Bioregenerative Life Support Experiment in the Lunar Palace 1 – Yi Sun – 40th COSPAR Scientific Assembly

“In this study, the development and succession of the microbial communities of air, water system, plant system, and key facilities surfaces in Lunar Palace 1 were continuously monitored and analyzed by using plate counting method and molecular biological method during the 90-day experiment.”

The viability of native microbial communities in martian environment (model) – Vorobyova, Elena – 40th COSPAR Scientific Assembly

“It was shown that in simulated conditions close to the parameters of the Martian regolith, the diversity of natural bacterial communities was not decreased, and in some cases the activation of some bacterial populations occurred in situ.”

Food microbiology

Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine – Joanita Sulaiman – Frontiers in Microbiology

“Whole genome shotgun (WGS) method revealed that the fermentation brine was dominated by the bacterial genus Weissella and later dominated by the fungal genus Candida.”

Transcriptomics/metagenomics

Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities – Leyden Fernandez – BMC Genomics

“We have here characterized and analyzed the metaregulome of three different environments, as well as their impact in the adaptation to particular variable physico-chemical conditions. “

Other microbiology

Inverse Correlation Between Helicobacter pylori Colonization and Obesity in a Cohort of Inner City Children – Hanh D. Vo – Helicobacter

“Our findings in a North American cohort are in agreement with studies from Asia and Europe suggesting that H. pylori infection decreases the prevalence of obesity in children.”

Microbes in the news

* Podcast: Your Home, Your Bacteria – Science Friday

“Jack Gilbert… is trying to develop a better understanding of the way people, bacteria, and the environment around them interact, from the kitchen floor to the greater Chicago area.”

Landmark Crohn’s Microbiome Study Yields Important Findings – David Wild – GastroEndoNews

“The association suggests that there is a potential link between the presence of these microbes and the serologic biomarkers, but that needs to be determined in future studies,” said Dr. Xavier, who presented the study at Digestive Disease Week 2014”

Is that how the capsules will look like? Good news: You can take your fecal transplants orally – Rachel Feltman – Washington Post

“In a study published Saturday in the Journal of the American Medical Association, researchers report that the same success rate can be reached by processing the healthy excrement into capsules and administering the pills by mouth.“

Probiotics on the brain: A growing number of scientists now believe that gut bacteria can influence mental health – Elizabeth Gehrman – Boston Globe

“Whenever someone says there’s an impossibility in medicine,” says Williams, “they end up being corrected in a few years.”

Unravelling the link between gut bacteria and horse health – University of Surrey

“Researchers at the University of Surrey, in collaboration with colleagues from Reading and Liverpool universities, have been awarded £100,000 funding by Petplan Charitable Trust… to create a laboratory model of the horse’s hindgut.”

The Second Brain: Gut Bacteria Control Human Behavior to Get the Best Nutrients – David Gutierrez – Epoch Times

“Bacteria within the gut are manipulative,” researcher Carlo Maley, PhD, said. “There is a diversity of interests represented in the microbiome, some aligned with our own dietary goals, and others not.”

Science, publishing, career

Sometimes My Job Seems Like a Secret – Amy Davidson – Speaking Of Research

“You are going to hell.” “You are a horrible person.” “We cannot be friends anymore.”

Sell yourself: Adding substance to your personal statement – Brian Rybarczyk – Science Careers at Science Magazine

“Obtaining feedback on your personal statement (or any piece of writing) can be intimidating, but feedback is essential for creating a polished and readable document.”

Bik’s Picks

Why Orange Juice Tastes Disgusting After You Brush Your Teeth: Finally, an answer – Sarah Fecht – Popular Science

“In a handy video, the American Chemical Society has explained why orange juice (and food in general) tastes like soap after you brush your teeth. “

[hr]

Non-human microbiome digest, October 6, 2014

Posted on October 6, 2014 by eliesbik

Microbiomes of cats with diabetes, vaginas of ewes and cows, chickens, hoopoes, Drosophila, sponges, plants, and subways.

Mammal Microbiome

* Faecal Microbiota of Cats with Insulin-Treated Diabetes Mellitus – Erin T. Bell – PLOS ONE

“Faecal samples were collected from insulin-treated diabetic and non-diabetic cats, and Illumina sequencing of the 16S rRNA gene and quantitative PCR were performed on each sample. “

* Characterization of the vaginal microbiota of ewes and cows reveals a unique microbiota with low levels of lactobacilli and near-neutral pH – JD Swartz, M Lachman, K Westveer, T O’Neill, T Geary – Frontiers in Veterinary Science

“We amplified and sequenced the V3-V4 region of the 16S ribosomal RNA contents yielding a total of 907,667 high-quality reads. “

Avian microbiome

* The chicken gastrointestinal microbiome – Brian B. Oakley – FEMS Microbiology Letters

“In this mini-review, we provide an overview of the current state of knowledge of the chicken GI microbiome focusing on spatial and temporal variability, the presence and importance of human pathogens, the influence of the microbiota on the immune system, and the importance of the microbiome for poultry nutrition.”

Environmental Factors Shape the Community of Symbionts in the Hoopoe Uropygial Gland More than Genetic Factors – Magdalena Ruiz-Rodríguez – Applied and Environmental Microbiology

“By disentangling the diversity of bacterial strains from the uropygium of hoopoes (Upupa epops) due to genetic relatedness or to a common environment, we explored the importance of horizontal (from the environment) and vertical (from parents) acquisition of antimicrobial-producing symbionts in this species.”

Insect Microbiome

Metagenome-Wide Association of Microbial Determinants of Host Phenotype in Drosophila melanogaster – John M. Chaston – mBio

“Monoassociation with bacteria that ectopically expressed a predicted oxidoreductase or gluconate dehydrogenase conferred reduced Drosophila TAG contents relative to the TAG contents in empty vector controls.”

Invertebrate microbiome

* Microbial Communities and Bioactive Compounds in Marine Sponges of the Family Irciniidae—A Review – Cristiane C. P. Hardoim and Rodrigo Costa – Marine Drugs

“The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. “

Plant microbiome

Microbial genome-enabled insights into plant–microorganism interactions – David Guttman, Alice C. McHardy & Paul Schulze-Lefert – Nature Reviews Genetics

“… culture-independent community profiling methods, coupled with metagenomic and metatranscriptomic studies, have provided the first insights into the emerging field of research on plant-associated microbial communities.”

Soil microbiome

Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland – Antje Gittel – Frontiers in Microbiology

“We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities.”

Water microbiome

Illuminating Microbial Dark Matter in Meromictic Sakinaw Lake – Esther A. Gies – Applied and Environmental Microbiology

“Here we describe diversity, abundance, and cooccurrence patterns of uncultivated microbial communities inhabiting the permanently stratified waters of meromictic Sakinaw Lake, British Columbia, Canada, using 454 sequencing of the small-subunit rRNA gene with three-domain resolution.”

Microbiome of the built environment

* Indoor-Air Microbiome in an Urban Subway Network: Diversity and Dynamics – Marcus H. Y. Leung – Applied and Environmental Microbiology

“Overall, subway lines harbored different phylogenetic communities based on α- and β-diversity comparisons, and closer inspection suggests that each community within a line is dependent on architectural characteristics, nearby outdoor microbiomes, and connectedness with other lines. “

[hr]

Non-human microbiome digest, October 2, 2014

Posted on October 2, 2014 by eliesbik

Microbiomes of mares with colic, corals and ascidians, bacteria in plant seeds, ciprofloxacin in compost, and yeast in Turkish sausages.

Mammal microbiome

Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods – Timothy J. Snelling – PLOS ONE

“Sequences mapping to rumen 16S rRNA and mcrA gene references were extracted from Illumina metagenome data.“

* Temporal changes and the effect of subtherapeutic concentrations of antibiotics in the gut microbiota of swine – Devin B. Holman – FEMS Microbiology Ecology

“In this study, the effect of two antibiotics on the swine gut microbiota over a 19-week monitoring period was investigated using Illumina-based sequencing. “

Changes in the faecal microbiota of mares precede the development of postpartum colic –
J. S. Weese – Equine Veterinary Journal

“Next generation sequencing of the V4 region of the 16S rRNA gene was performed on samples from 13 mares that developed colic, 13 mares that did not display colic, and 5 non-pregnant controls.”

Bird microbiome

Correlations between changes in intestinal microbiota composition and performance parameters in broiler chickens – L. A. Rubio – Journal of Animal Physiology and Animal Nutrition

“The composition of the intestinal microbiota was analysed by qPCR at different points of the intestinal tract, and a number of nutritional parameters were also determined.”

Insect microbiomes

Differential Genome Evolution Between Companion Symbionts in an Insect-Bacterial Symbiosis – Gordon M. Bennett – mBio

“To understand how symbiont genome degeneration proceeds, we compared the genomes of symbionts in two leafhopper species”

Metagenome-Wide Association of Microbial Determinants of Host Phenotype in Drosophila melanogaster – John M. Chaston – mBio

“.. we measured two microbiota-responsive host traits, development time and triglyceride (TAG) content, in Drosophila melanogaster flies monoassociated with each of 41 bacterial strains.”

Invertebrate microbiome

Quorum Sensing Signal Production and Microbial Interactions in a Polymicrobial Disease of Corals and the Coral Surface Mucopolysaccharide Layer – Beth L. Zimmer – PLOS ONE

“These findings demonstrate for the first time that AHLs are present in an active coral disease.”

The secret to a successful relationship: lasting chemistry between ascidians and their symbiotic bacteria – Eric W. Schmidt – Invertebrate Biology

Plant microbiome

Plants prepackage beneficial microbes in their seeds – Phys.org

“The researchers, from the University of Notre Dame, presented their findings today at the 5th ASM Conference on Beneficial Microbes.”

Cave microbiome

* Mycobiome of the Bat White Nose Syndrome Affected Caves and Mines Reveals Diversity of Fungi and Local Adaptation by the Fungal Pathogen Pseudogymnoascus (Geomyces) destructans – Tao Zhang – PLOS ONE

“This study was conducted in 2010–2011 in New York and Vermont using 90 samples from four mines and two caves situated within the epicenter of WNS. “

Soil and sediment microbiome

Differential distribution and abundance of diazotrophic bacterial communities across different soil niches using a gene-targeted clone library approach – Basit Yousuf – FEMS Microbiology Letters

“Differential occurrence of diazotrophs was studied by the nifH gene-targeted clone library approach.”

Spatiotemporal Analysis of Bacterial Diversity in Sediments of Sundarbans Using Parallel 16S rRNA Gene Tag Sequencing – Pijush Basak – Microbial Ecology

“The total sediment DNA was extracted and subjected to the 16S rRNA gene pyrosequencing, which resulted in 117 Mbp of data from three experimental stations. “

Ciprofloxacin residues in municipal biosolids compost do not selectively enrich populations of resistant bacteria – Caitlin P. Youngquist – Applied and Environmental Microbiology

“Regression analysis showed that growth of the susceptible strain of E. coli can be reduced given a sufficiently high concentration of ciprofloxacin (P<0.007), a result that is consistent with adsorption being the primary mechanism of sequestration. “

Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally – Kelly S. Ramirez – Proceedings of the Royal Society B

“Here, we present an assessment of soil biodiversity and biogeographic patterns across Central Park in New York City that spanned all three domains of life, demonstrating that even an urban, managed system harbours large amounts of undescribed soil biodiversity.”

Water microbiome

Abundance and Dynamics of Antibiotic Resistance Genes and Integrons in Lake Sediment Microcosms – Björn Berglund – PLOS ONE

“Resistance genes sulI and ermB were quantified in the microcosm sediments with mean abundances 5 and 15 gene copies/106 16S rRNA gene copies, respectively. “

Microbial composition of the activated sludge of Moscow wastewater treatment plants
A. Yu. Kallistova – Microbiology

“FISH investigation revealed that aerobic sludge were eubacterial communities; the metabolically active archaea contributed insignificantly.”

Phytoplankton, bacterioplankton and virioplankton structure and function across the southern Great Barrier Reef shelf – Daniel M. Alongi – Journal of Marine Systems

“Phytoplankton, bacteria and virus dynamics are driven by across-shelf changes in water chemistry and hydrography.”

Food microbiology

Pulque production from fermented agave sap as a dietary supplement in Prehispanic Mesoamerica – Marisol Correa-Ascencio – PNAS

“A novel bacterial lipid biomarker approach is reported, which provides a new means of documenting the consumption of bacterially fermented alcoholic beverages in antiquity worldwide.”

Biodiversity of Yeast Mycobiota in “Sucuk,” a Traditional Turkish Fermented Dry Sausage: Phenotypic and Genotypic Identification, Functional and Technological Properties – Ismet Ozturk, and Osman Sagdic – Journal of Food Science

“The yeast isolates were determined as genotypic using 2 different polymerase chain reaction (PCR) methods (rep-PCR and RAPD-PCR).”

[hr]

General microbiology and science, September 29, 2014

Posted on September 29, 2014 by eliesbik

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

Metabolomics

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

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

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

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

Metagenomics

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

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

Phages and viruses

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

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

Ecology / Bioinformatics

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

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

Techniques

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

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

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

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

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

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

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

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

More microbiology

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

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

Microbes in the News

Scientists sniffing out the Western allergy epidemic – BBC News

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

Study looks at bacteria on a plane – CNN Wire

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

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

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

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

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

Science and Art

Should Silicon Valley Hire Microbes? – Glenn McDonald – Discovery

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

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

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

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

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

Bik’s Picks

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

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

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

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

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

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

[hr]

Microbiome digest, September 25, 2014

Posted on September 25, 2014 by eliesbik

[hr]

Asbestos and microbiome, human gut microbiome during a long stay in the hospital, gut microbiome of 15 mammals, Wolbachia in insects, microbiome of plant roots, and eukaryotes in Norwegian waters.

Human respiratory microbiome

Airways microbiota: Hidden Trojan horses in asbestos exposed individuals? – Dimitrios E. Magouliotis – Medical Hypotheses

“Here, we propose and discuss that certain proteins secreted by airways symbiotic microbiota create membrane pores to the airway epithelial cells, through which asbestos fibers can penetrate the lung parenchyma and reach the sub-pleural areas.”

Human gut microbiome

Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness – Alexander Zaborin – mBio

“We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients.”

Mammal microbiome

Convergence of gut microbiomes in myrmecophagous mammals – Frederic Delsuc – Molecular Ecology

“Here, we expand upon previous mammalian gut microbiome studies … to characterize the composition of gut microbiota in 15 species representing all placental myrmecophagous lineages and their close relatives from zoo- and field-collected samples.

Insect microbiome

Symbionts Commonly Provide Broad Spectrum Resistance to Viruses in Insects: A Comparative Analysis of Wolbachia Strains – Julien Martinez – PLOS Pathogens

“We have investigated antiviral protection in 19 Wolbachia strains originating from 16 Drosophila species after transfer into the same genotype of Drosophila simulans. “

Plant microbiome

Niche and host-associated functional signatures of the root surface microbiome – Maya Ofek-Lalzar – Nature Communications

“Metagenomic (genetic potential) analysis identifies a core set of functional genes associated with root colonization in both plant hosts, and metatranscriptomic (functional expression) analysis revealed that most genes enriched in the root zones are expressed. “

Water microbiome

Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing – Elianne S. Egge – Journal of Eukaryotic Microbiology

“Nano- and picoplanktonic subsurface samples were collected monthly for 2 yr, and the haptophytes were targeted by amplification of RNA/cDNA with Haptophyta-specific 18S ribosomal DNA V4 primers. “

Microbes in the news

Intensive Loss of Gut Bacteria Diversity – Molly Sharlach – The Scientist

In a study published today (September 23) in mBio, researchers also fed ICU patients’ “ultra-low-diversity” gut microbes to C. elegans roundworms.

How Termites Evolved to Decompose Plant Matter: Gut Bacteria and Fungus – Catherine Griffin – Science World Report

“In order to better understand this interaction, the researchers analyzed plant decomposition genes in the first genome sequencing of a fungus-farming termite and its fungal crop, and bacterial gut communities.”

Science and Career

Scientists Are Not Trusted By Americans – Here’s Why – Science 2.0

“A paper in PNAS finds that Americans seem wary of researchers because they get grant funding and do not trust scientists pushing political and cultural agendas. “

Read The Nasty Comments Women In Science Deal With Daily – Macrina Cooper-White – Huffington Post

“Every day you’re faced with some comment, some snide remark, some inability to get a name on a research paper. “

Bik’s Picks

Water on Earth is older than the sun, scientists say – Deborah Netburn – Los Angeles Times

“Some of the water molecules in your drinking glass were created more than 4.5 billion years ago, according to new research.”

Science Graphic of the Week: Three Ways to Visualize Our Melting Northern Ice Cap – Nick Stockton – Wired.com

“These three visualizations, by NASA’s Scientific Visualization Studio, illustrate this steadily unfolding situation, which has nightmarish implications..“

Healthy food might be bad for patients – here’s why – Amanda Squire – The Conversation

“The truth is that healthy food as we think of it may not be what patients really need.”

Brazil releases ‘good’ mosquitoes to fight dengue fever – BBC News

“Brazilian researchers in Rio de Janeiro have released thousands of mosquitoes infected with bacteria that suppress dengue fever.”

[hr]

	Francis W on The Hetch Hetchy Railroad
	Best Practice Exchan… on June 1, 2018
	May 17, 2024 \| Micro… on May 15, 2024
	Kathy Brown on The Hetch Hetchy Railroad
	John Wilbur on The Hetch Hetchy Railroad

Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Category Archives: Built Environment Microbiology

Microbiome digest, December 8, 2014

Microbiome digest, November 20, 2014

Microbiome digest, November 18, 2014

Microbiome digest, November 5, 2014

Non-human microbiome digest, October 28, 2014

Microbiome digest, October 13, 2014

Non-human microbiome digest, October 6, 2014

Non-human microbiome digest, October 2, 2014

General microbiology and science, September 29, 2014

Microbiome digest, September 25, 2014