Category Archives: Plant Root Soil microbiome

Microbiome digest, November 5, 2014

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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.”

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Microbiome digest, November 3, 2014

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Human oral and vaginal microbiomes, rumen microbiome of impalas, sample handling and sponges, and two remarkable pieces in the New York Times.

Human oral microbiome

The association between the upper digestive tract microbiota by HOMIM and oral health in a population-based study in Linxian, China – Guoqin Yu – BMC Public Health

“Human Oral Microbe Identification Microarrays were used to test for the presence of 272 human oral bacterial species (97 genera) in upper digestive tract (UDT) samples collected from 659 participants. “

Pregnancy and birth microbiome

Poster: Comparison of the Vaginal Microbiomes of Pregnant Women of Four Ethnicities
and Identification of Taxa Associated with Urogenital Disease – Mendz GL – ECCMID Poster

“Principal component analysis suggested differences in the bacterial populations of healthy women and those with genital infections, with clustering of the latter along the Protobacteria axis “

Animal microbiome

Examination of the Rumen Bacteria and Methanogenic Archaea of Wild Impalas (Aepyceros melampus melampus) from Pongola, South Africa – Laura M. Cersosimo – Microbial Ecology

“In the present study, next-generation sequencing and real-time polymerase chain reaction were used to investigate the diversity and density of the bacteria and methanogenic archaea residing in the rumen of five adult male impalas”

Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges – Cristiane C. Hardoim – Frontiers in Microbiology

Bacterial community profiling of the sympatric keratose species Sarcotragus spinosulus and Ircinia variabilis (Dictyoceratida, Irciniidae) was performed by polymerase chain reaction-denaturing gradient gel electrophoresis and 454-pyrosequecing of 16S rRNA gene fragments. “

Plant microbiome

Soil type-dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce – Susanne Schreiter – FEMS Microbiology Ecology

“16S rRNA gene fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. “

Are heterotrophic and silica-rich eukaryotic microbes an important part of the lichen symbiosis? – David M Wilkinson – Mycology: An International Journal on Fungal Biology

“In this necessarily speculative paper we highlight areas for future research and how newer technologies may be useful for understanding the full suite of organisms involved in the lichen symbiosis.”

Soil microbiome

Selection on soil microbiomes reveals reproducible impacts on plant function – Kevin Panke-Buisse – ISME Journal

“Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment.”

Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA – Magdalena R. Osburn – Frontiers in Microbiology

“Geochemical data, energetic modeling, and DNA sequencing were combined with principle component analysis to describe this deep (down to 8100 ft below surface), terrestrial environment.”

Bioinformatic tools

* Seeing the forest for the genes: Using metagenomics to infer the aggregated traits of microbial communities – Noah Fierer – Frontiers in Microbiology

“Microbial ecologists could benefit by borrowing the concept of community-aggregated traits (CATs) from plant ecologists to glean more insight from the ever-increasing amount of metagenomic data being generated.”

Metabolomics

Fructan supplementation of senior cats affects stool metabolite concentrations and fecal microbiota concentrations, but not nitrogen partitioning in excreta – K.A. Barry – Journal of Animal Science

“Fructan supplementation may benefit senior cats as it modulates stool odor-forming compounds and decreases some protein catabolites and pathogenic gut microbiota concentrations without affecting N retention.”

Proteomics

From the Banfield lab: Development of an enhanced metaproteomic approach for deepening the microbiome characterization in the human infant gut – Weili Xiong – Journal of Proteome Research

“….we have designed a novel metaproteomic strategy based on double filtering (DF) the raw samples, a method that fractionates microbial from human cells to enhance microbial protein identification and characterization in complex fecal samples from healthy premature infants. “

More microbiology

Complementarity between targeted real-time specific PCR and conventional broad-range 16S rDNA PCR in the syndrome-driven diagnosis of infectious diseases – A.-S. Morel – European Journal of Clinical Microbiology & Infectious Diseases

“Herein, we report our experience in the diagnosis of infectious diseases over two years, during which 32,948 clinical samples from 18,056 patients were received from France and abroad.”

Microbes in the news

* There Is No ‘Healthy’ Microbiome – Ed Yong – New York Times

“The microbiome is complex, varied, ever changing and context-dependent — qualities that are the enemies of easy categorization.”

Study: Ice Man has traces of bacteria that undermined his health – BetaWired

“…they found evidence of the presence of Treponema denticola, an opportunistic pathogen implicated in the development of periodontal diseases. “

Science, publishing, and career

How Do Small Things Make a Big Difference? Activities to Teach about Human–Microbe Interactions – Chandana Jasti – The American Biology Teacher

“In these guided inquiry activities, students investigate human–microbe interactions as they work together to interpret and analyze authentic data from published articles and develop scientific models.”

2014 Life Sciences Salary Survey – Jyoti Madhusoodanan – The Scientist

“This year’s data reveal notable variation in compensation for life scientists working in different fields, sectors, and regions of the world.”

Academic Science Isn’t Sexist – Wendy M. Williams and Stephen J. Ceci – New York Times

“Our analyses show that women can and do prosper in math-based fields of science, if they choose to enter these fields in the first place.”

and two rebuttals:
Academic science is sexist: We do have a problem here – Emily Willingham
* The flawed and offensive logic of “Academic Science Isn’t Sexist” in the @nytimes – Jonathan Eisen – The Tree of Life

Bik’s Picks

Standing time and all-cause mortality in a large cohort of Australian adults – Hidde P. van der Ploeg – Preventive Medicine

“Increasing standing may hold promise for alleviating the health risks of prolonged sitting.”

A Face to Remember – Kerry Grens – The Scientist

“Once dominated by correlational studies, face-perception research is moving into the realm of experimentation—and gaining tremendous insight.”

* With a very cute picture: Rovers Disguised as Baby Penguins Can Quietly Infiltrate Penguin Colonies – Rachel Nuwer – Smithsonian

“Pursuing this hunch, they outfitted the rover with a big ball of fluff and a little penguin head and arms. ”

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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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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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Microbiome digest, October 22, 2014

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Microbes in the mouth of patients with heart disease, bile and gall bladder microbiome of pigs, precisely restoring resistance to Clostridium difficile infection, and networks between fungi and plants. And don’t forget the solar eclipse tomorrow PM for most of the US.

Human oral microbiome

Microbial Diversity Similarities in Periodontal Pockets and Atheromatous Plaques of Cardiovascular Disease Patients – Wagner Serra e Silva Filho – PLOS ONE

“Subgingival biofilm and coronary balloons used in percutaneous transluminal coronary angioplasty were collected from 18 subjects presenting with generalized moderate to severe periodontitis and OCAA. DNA was extracted and the gene 16S was amplified, cloned and sequenced.”

Human gut microbiome

Dietary Patterns Differently Associate with Inflammation and Gut Microbiota in Overweight and Obese Subjects – Ling Chun Kong – PLOS ONE

“We aimed to characterize dietary patterns in overweight and obese subjects and evaluate the different dietary patterns in relation to metabolic and inflammatory variables as well as gut microbiota.”

Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men – Anne Salonen – ISME Journal

“Here we report a comprehensive and deep microbiota analysis of 14 obese males consuming fully controlled diets supplemented with resistant starch (RS) or non-starch polysaccharides (NSPs) and a weight-loss (WL) diet.”

Animal models of microbiome research

* Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile – Charlie G. Buffie – Nature

“..we determine that Clostridium scindens, a bile acid 7α-dehydroxylating intestinal bacterium, is associated with resistance to C. difficile infection and, upon administration, enhances resistance to infection in a secondary bile acid dependent fashion.”

* Changes in the Bacterial Microbiota in Gut, Blood, and Lungs following Acute LPS Instillation into Mice Lungs – Marc A. Sze – PLOS ONE

“Bacterial microbiota of the bronchoalveolar lavage fluid, blood, and cecum were determined using 454 pyrotag sequencing and quantitative polymerase chain reaction (qPCR) at 4 through 168 hours post-instillation.”

Specific Microbiome Changes in a Mouse Model of Parenteral Nutrition Associated Liver Injury and Intestinal Inflammation – J. Kirk Harris – PLOS ONE

“Microbiome analysis in the PNALI mouse identified specific alterations within colonic microbiota associated with PNALI and further association of these communities with the lipid composition of the PN solution. “

Animal microbiome

Characterization of the bile and gall bladder microbiota of healthy pigs – Esther Jiménez – Microbiology Open

“We have studied, by culture-dependent techniques and a 16S rRNA gene-based analysis, the microbiota present in the bile, gall bladder mucus, and biopsies of healthy sows”

Characterization of Egg Laying Hen and Broiler Fecal Microbiota in Poultry Farms in Croatia, Czech Republic, Hungary and Slovenia – Petra Videnska – PLOS ONE

“In this study we were therefore interested in the prevalence of selected antibiotic resistance genes and microbiota composition in feces of egg laying hens and broilers originating from 4 different Central European countries determined by real-time PCR and 16S rRNA gene pyrosequencing, respectively. “

Plant microbiome

* Assembly of complex plant–fungus networks – Hirokazu Toju – Nature Communications

“The examined symbiotic network of a temperate forest in Japan includes 33 plant species and 387 functionally and phylogenetically diverse fungal taxa, and the overall network architecture differs fundamentally from that of other ecological networks. “

Soils and sediments

The long-term adaptation of bacterial communities in metal-contaminated sediments: a metaproteogenomic study – David C. Gillan – Environmental Microbiology

“Two freshwater sites, Férin and MetalEurop, differing by one order of magnitude in metal levels (MetalEurop: 3218 mg Zn kg−1; 913 mg Pb kg−1) were compared by shotgun metaproteogenomics. “

Bioinformatics / metabolomics

* Biogeochemical Typing of Paddy Field by a Data-Driven Approach Revealing Sub-Systems within a Complex Environment – A Pipeline to Filtrate, Organize and Frame Massive Dataset from Multi-Omics Analyses – Diogo M. O. Ogawa – PLOS ONE

“We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. “

Estimating coverage in metagenomic data sets and why it matters – Luis M Rodriguez-R and Konstantinos T Konstantinidis – ISME Journal

“We demonstrate here how available solutions can determine the level of sequencing coverage obtained by metagenomic data sets and thus, guide their robust analysis and comparison.”

Immunology

* Fall issue of Stanford Medicine reports on the immune system’s balancing act

“If you want to understand the human immune system, try studying humans — not mice, urges Mark Davis, PhD, in a special report on the immune system in the new issue of Stanford Medicine magazine.”

Bik’s Picks

Genome sequence of a 45,000-year-old modern human from western Siberia – Qiaomei Fu – Nature

“the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. “

Sky spectacle: Partial solar eclipse coming Thursday – USA Today

“In the afternoon, a partial solar eclipse — where the moon covers a part of the sun — will be visible across much of the USA, barring any pesky clouds that could block the show.”

Go Giants! The Science of Baseball – Exploratorium

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Microbiome digest, October 21, 2014

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Human oral microbiome

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

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

Human respiratory microbiome

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

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

Human gut microbiome

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

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

Pregnancy and birth

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

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

Animal microbiome

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

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

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

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

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

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

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

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

Bioreactor microbiome

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

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

Metagenomics / Transcriptomics / Bioinformatics

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

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

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

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

Microbial Ecology

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

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

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

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

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

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

More microbiology

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

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

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

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

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

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

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

Techniques

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

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

Microbes in the news

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

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

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

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

Building houses with bacteria – Euronews

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

Bik’s Picks

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

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

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

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

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

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

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

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

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Microbiome Digest, October 20, 2014

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Oral core microbiome, symbionts in crabs, sponges, and Drosophila, metabolites in dolphin’s breath, and retraction of a paper favored by Dr. Oz.

Pregnancy and birth

NEC in Twin Pregnancies: Incidence and Outcomes – Sathyaprasad C Burjonrappa, Brian Shea, Diya Goorah – Journal of Neonatal Surgery

“There is a remarkable higher incidence of NEC amongst twins. Abnormal colonization of the gastrointestinal tract appears to be an immediate postpartum event.”

Human oral microbiome

Intraindividual variation in core microbiota in peri-implantitis and periodontitis – Noriko Maruyama – Scientific Reports

“To improve our knowledge of the different communities of complex oral microbiota, we compared the microbial features between peri-implantitis and periodontitis in 20 patients with both diseases. “

Antimicrobial Effect of Lemongrass Oil against Oral Malodor Microorganisms and the Pilot Study of Safety and Efficacy of Lemongrass Mouthrinse on Oral Malodor – Panitta Satthanakul – Journal of Applied Microbiology

“Antimicrobial activity of LG mouthrinse was examined against common odorigenic microorganisms using broth microdilution assay and the disc diffusion method. A randomized double-blind clinical study was performed in 20 healthy volunteers.”

Animal microbiome

Molecular evidence of digestion and absorption of epibiotic bacterial community by deep-sea crab Shinkaia crosnieri – Tomo-o Watsuji – ISME Journal

“A phylogenetic analysis showed that many of the bacterial 16S ribosomal RNA gene sequences obtained from the intestine were closely related to the sequences of the epibionts, thus they were probably derived from the epibionts.”

* In vivo function and comparative genomic analyses of the Drosophila gut microbiota identify candidate symbiosis factors – Peter D. Newell – Frontiers in Microbiology

“We compared microbiota isolates with con-specific or closely related bacterial species isolated from non-fly environments. “

* Two distinct microbial communities revealed in the sponge Cinachyrella – Marie L. Cuvelier – Frontiers in Microbiology

“Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rDNA tag pyrosequencing.”

* Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality – Fan Zhang – FEMS Microbiology Ecology

“PCR cloning and sequencing of archaeal 16S rRNA and amoA genes showed that the archaeal community composition and structure were different from that in seawater and varied among sponge species. “

Plant microbiome

Reduced dependence of rhizosphere microbiome on plant-derived carbon in 32-year long-term inorganic and organic fertilized soils – Chao Ai – Soil Biology and Biochemistry

“Wheat rhizosphere microbiome was studied by stable isotope probing and pyrosequencing.”

Environmental microbiome

Characterization of bacterial communities associated with seasonal water masses from Tongyoung in South Sea of Korea – Sung-Suk Suh – Ocean Science Journal

“In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with two different water masses from Tongyoung in the South Sea of Korea. “

Bacterial community structure of a lab-scale anammox membrane bioreactor – Alejandro Gonzalez-Martinez – Biotechnology Progress

“In this study, next-generation sequencing techniques have been used for the investigation of the bacterial communities of this MBR Anammox for the first time ever. “

Metagenomics & Bioinformatics

GenomePeek: What exactly is that sequencing data? – Katelyn McNair – MicroBEnet

“I wrote the initial version of GenomePeek, and tested it with various data sets using this student’s data. I quickly found that some genes work better than others, and so currently the four genes analyzed are: 16S, recA, rpoB, and groEL.”

Metabolomics

Metabolite Content Profiling of Bottlenose Dolphin Exhaled Breath – Alexander A. Aksenov – Analytical Chemistry

“We have developed a method to reproducibly sample breath from small cetaceans, specifically Atlantic bottlenose dolphins (Tursiops truncatus). “

Proteomics

Symbiosis, Dysbiosis and Rebiosis – the value of metaproteomics in human microbiome monitoring – Lei Mao and Jacqueline Franke – Proteomics

“After a brief review of the history and state-of-the-art of metaproteomics in the field of environmental health research, focus of this perspective article will be put on the role of cross-species joint efforts in symbiosis, dysbiosis and rebiosis of the human gut during human development, pathogenesis and aging.”

More microbiology

Bridging the gap between viable but non-culturable and antibiotic persistent bacteria – Mesrop Ayrapetyan – Trends in Microbiology

“This discussion is intended to stimulate discourse about these seemingly different but very similar dormant states.”

* Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite
Zhang Wang, Martin Wu – PLOS ONE

“Using a phylogenomic approach and leveraging on the increased taxonomic sampling of alphaproteobacterial and eukaryotic genomes, we reconstructed the metabolisms of both proto-mitochondria and pre-mitochondria.”

Real-time video imaging as a new and rapid tool for antibiotic susceptibility testing by the disk diffusion method: a paradigm for evaluating resistance to imipenem and identifying extended-spectrum β-lactamases – Stéphanie Le Page – International Journal of Antimicrobial Agents

“..we present here for the first time video movies of the appearance of the diameter of inhibition by the disk diffusion in real-time. “

Microbes in the news

Can Microbes Help Feed the World? – Amy Mayer – BioScience

“To help meet the challenge for food, scientists are using new technologies to better understand the role that soil microbes might play in bolstering agricultural production. “

Dentists Want To See Studies On Pot-Cavity Link – CBS Local

“Patients are experiencing tooth decay, expensive dentist bills and the pain of dealing with it all. The biggest side effect is dry mouth.”

Bik’s Picks

Brain surgery, by robot, through the cheek – Science Daily

“Engineers have developed a surgical robot designed to perform brain surgery by entering through the cheek instead of the skull that can operate on a patient in an MRI scanner. Additionally, the engineers have designed the system so that much of it can be made using 3-D printing in order to keep the price low.”

* Hilarious cartoons on Imgur: Real Scientists vs. Movie Scientists 

* Authors retract green coffee bean diet paper touted by Dr. Oz – Ivan Oransky – Retraction Watch

“Two authors of a 2012 paper sponsored by a company that made grand claims about green coffee bean extract’s abilities to help people lose weight have retracted it. The study was cited by The Dr. Oz Show, and last month it cost the company a $3.5 million settlement with the Feds.”

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Non-human microbiome digest, October 6, 2014

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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. “

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Microbiome Digest, October 3, 2014

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Antibiotics in the first 24 months of life associated with obesity, Giant Pandas are no cul-de-sac, and microbiome and inflammatory disease. And lots of weekend reads!

Pregnancy and birth

Association of Antibiotics in Infancy With Early Childhood Obesity – L. Charles Bailey – JAMA Pediatrics

“Cumulative exposure to antibiotics was associated with later obesity …; this effect was stronger for broad-spectrum antibiotics”

Human gut microbiome

Faecal microbiota composition and host–microbe cross-talk following gastroenteritis and in postinfectious irritable bowel syndrome – Jonna Jalanka-Tuovinen – Gut

“Using a phylogenetic microarray and selected qPCR assays, we analysed differences in the faecal microbiota of 57 subjects from five study groups”

Animal models of microbiome research

Dietary modulation of the microbiome affects autoinflammatory disease – John R. Lukens – Nature

“Here we show that the intestinal microbiota of diseased Pstpip2cmo mice was characterized by an outgrowth of Prevotella. “

Mammal microbiome

Giant pandas are not an evolutionary cul-de-sac: Evidence from multidisciplinary research
Fuwen Wei – Molecular Biology and Evolution

“The latest and most advanced research shows that giant pandas are successful animals highly adapted to a specialized bamboo diet via morphological, ecological and genetic adaptations and co-adaptation of gut microbiota.”

Plant microbiome

Multi-symbiotic systems: functional implications of the coexistence of grass–endophyte and legume–rhizobia symbioses – Pablo A. García Parisi – Oikos

“After five months, we quantified the number of nodules in Trifolium roots, shoot biomass of both plant species, and the contribution of atmospheric nitrogen fixation vs. soil nitrogen uptake to above ground nitrogen in each plant species. “

Microbes in the news

Young companies, big ideas – The 2014 edition of the CNN 10: Startups – CNN

“Her doubts were assuaged when supporters donated $350,000 to help launch her startup, uBiome. Now, two years later, uBiome is exploring an emerging field of human biology while giving users a glimpse into how their bodies work.”

No women, unfortunately! And they did not accept my application to be a judge either. MO BIO Laboratories, Inc. announces Microbiome Awards winners – PR NewsWire

“MO BIO Laboratories, Inc. is proud to announce the winners of the MO BIO Microbiome Awards, which provide young, extraordinary scientists with funding and recognition to carry out scientific work in the field of microbiome research.”

Super-bacteria are growing in space … and we’re the ones breeding them – Meera Senthilingam – CNN

“You might think of space as a germ-free environment, but microbes can be carried to space inside human gut flora as well as in food and water and once up there, can be expelled by humans in their breath.”

There’s a simple way to stop the spread of antibiotic-resistant bacteria – Melinda Mary Pettigrew – Washington Post

“The issue boils down to this: we use too many antibiotics. Studies show that up to half of all antibiotics are prescribed unnecessarily.”

Across Indian zoos, rat pee spreading bacteria, killing big cats: Scientists – Priyangi Agarwal – The Times of India

“The leptospirosis bacteria, found in rodent urine, makes its way into blood samples of zoo animals and causes higher morbidity and mortality, scientists at the Indian Veterinary Research Institute (IVRI) in Bareilly have found. “

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

“Brazilian researchers in Rio de Janeiro have released thousands of mosquitoes infected with bacteria that suppress dengue fever. The hope is they will multiply, breed and become the majority of mosquitoes, thus reducing cases of the disease.“

Science, Publishing, and Career

Young, Brilliant and Underfunded – Andy Harris – New York Times

“The bulk of that money goes to researchers who are in many cases esteemed in their fields — but also, in many cases, beyond the age when most scientists make their most important contributions to their fields.”

Why women leave tech: It’s the culture, not because ‘math is hard’ – Kieran Snyder – Fortune

“Stories from 716 women who left tech show that the industry’s culture is the primary culprit, not any issues related to science education.”

Satire: Tips For Working With A Lab Partner – FakeScience

Bik’s Picks

Is this the end of autumn as we know it? – Stephanie Pappas – BBC Earth

“The study of the basic triggers of autumnal leaf changes, never mind the impact of climate change on these, is still in its infancy in part because scientists have traditionally focused their attentions on the seasonal changes in March and April than those later in the year.”

The Incredible Rubber Glove – Olga Khazan – The Atlantic

“Basic protective gear was revolutionary for 19th-century medicine, and health workers trying to stop Ebola are recognizing its importance all over again.”

This Is Why Your Voice Sounds So Frickin’ Weird To You – Macrina Cooper-White – The Huffington Post

“Have you ever listened to a recording of your own voice and thought, “Whoa. Do I really sound like that?” Well, it’s time to face the music. You really do.”

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Non-human microbiome digest, October 2, 2014

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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).”

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