Microbiome digest, November 12, 2014

Another short installment of the Digest. Two studies on microbial DNA contamination in reagents and laboratories, and gut microbiome in Down Syndrome.
Human gut microbiome

* Gut Microbiome in Down Syndrome – Elena Biagi – PLOS ONE

* Superresolution Imaging Captures Carbohydrate Utilization Dynamics in Human Gut Symbionts – Krishanthi S. Karunatilaka – mBio

Microbiota Talks Cholera out of the Gut – Amanda J. Hay, Jun Zhu – Cell Host & Microbe

 

Animal microbiome

Comparative Metagenomic Analysis of Coral Microbial Communities Using a Reference-Independent Approach – Camila Carlos – PLOS ONE

The Effect of Antibiotics on Associated Bacterial Community of Stored Product Mites – Jan Kopecky – PLOS ONE

 

Metagenomic Insights into the RDX-Degrading Potential of the Ovine Rumen Microbiome – Robert W. Li – PLOS ONE

Plant microbiome

Functional Potential of Soil Microbial Communities in the Maize Rhizosphere – Xiangzhen Li – PLOS ONE

* Genome-wide association study of Arabidopsis thaliana leaf microbial community – Matthew W. Horton – Nature Communications

Environmental microbiome

A method for sampling microbial aerosols using high altitude balloons – N.C. Bryan – Journal of Microbiological Methods

Techniques

(preprint already featured here in July, but now officially out)
* Reagent and laboratory contamination can critically impact sequence-based microbiome analyses – Susannah J Salter – BMC Biology

* Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data – Richard W. Lusk – PLOS ONE

 

Reconceptualising the beta diversity-environmental heterogeneity relationship in running water systems – Jani Heino – Freshwater Biology

Microbes in the news

* Contaminomics: Why Some Microbiome Studies May Be Wrong – Ed Yong – National Geographic

* The Kitome: Dealing with the reagent microbiome – Pat Schloss – Mothur.org

DNA Extraction Kits Contaminated – Kerry Grens – The Scientist

Bik’s Picks

Serotonin lies at the intersection of pain and itch – Bethany Brookshire – ScienceNews

Rainbow palette found in Brooklyn’s contaminated water – Aviva Rutkin – New Scientist

This did not work on my cats, but feel free to try:
‘Cat Circles’, The Amazing Phenomenon In Which a Cat Will Always Sit Inside a Circle on the Floor – Lori Dorn – Laughing Squid

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Microbiome digest, November 11, 2014

Human oral microbiome

Physiological Adaptations of Key Oral Bacteria – C. W. Ian Douglas – Advances in Microbial Physiology

Human gut microbiome

Development and Survival of Th17 Cells within the Intestines: The Influence of Microbiome- and Diet-Derived Signals – Joseph H. Chewning – The Journal of Immunology

Gut Inflammation and Immunity: What Is the Role of the Human Gut Virome? – Alfredo Focà – Mediators of Inflammation

Animal microbiome

Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change – Karlette A. Fernandes – PLOS ONE

The Effect of Phytochemical Tannins-Containing Diet on Rumen Fermentation Characteristics and Microbial Diversity Dynamics in Goats Using 16S rDNA Amplicon Pyrosequencing – B. R. Min – Agriculture, Food & Analytical Bacteriology

Microbial diversity in forestomach and caecum contents of the greater long-tailed hamster Tscherskia triton (Rodentia: Cricetidae) – Akio Shinohara – Mammalian Biology – Zeitschrift für Säugetierkunde

The pathogen Batrachochytrium dendrobatidis disturbs the frog skin microbiome during a natural epidemic and experimental infection – Andrea J. Jani – PNAS USA

Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk – Roberta M. O’Connor – PNAS USA

Arbuscular mycorrhizal fungi communities in a coral cay system (Morrocoy, Venezuela) and their relationships with environmental variables – M.M. Alguacil – Science of the Total Environment

Soil microbiome

Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities – Jun-Min Li – Scientific Reports

Impact of short-term storage temperature on determination of microbial community composition and abundance in aerated forest soil and anoxic pond sediment samples – Franziska B. Brandt – Systematic and Applied Microbiology

Seasonal influence of climate manipulation on microbial community structure and function in mountain soils – Jérémy Puissant – Soil Biology and Biochemistry

Effect of organic and conventional practices on carbon-substrate utilisation by the soil microbial community in a ‘Cripps Pink’/M7 apple orchard – Andre H Meyer – South African Journal of Plant and Soil

* The Soil Biota Composition along a Progressive Succession of Secondary Vegetation in a Karst Area – Jie Zhao – PLOS ONE

Effects of salinization and crude oil contamination on soil bacterial community structure in the Yellow River Delta region, China – Yong-chao Gao – Applied Soil Ecology

Water microbiome

Community dynamics of prokaryotic and eukaryotic microbes in an estuary reservoir – Zhen Sun – Scientific Reports

Microbial diversity and community structure across environmental gradients in Bransfield Strait, Western Antarctic Peninsula – Camila N. Signori – Frontiers in Microbiology

Metagenomics

Assessment of quality control approaches for metagenomic data analysis – Qian Zhou – Scientific Reports

PaperClip: rapid multi-part DNA assembly from existing libraries – Maryia Trubitsyna – Nucleic Acids Research

Microbial phylogeny

* Assessing the global phylum level diversity within the bacterial domain: A review – Noha H. Youssef – Journal of Advanced Research

Science, publishing, career

Crosspost: Using Google Scholar in Scholarly Workflows – Jonathan Eisen – microBEnet

Hilarious: Overly honest references: “Should we cite the crappy Gabor paper here?” – RetractionWatch – (Note: paper has been removed – see a screenshot here)

Microbes in the news

* Bacteria Hysteria? Deadly bacteria normally found in toilets was discovered in the microwave of these students – The Journal.ie

Bik’s Picks

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication – Michael J. Montague – PNAS USA

UCSF develops site to make sense out of sugar science – Erin Allday – SFGate

Found: The Ideal Fatness for Elephant Seals – Elizabeth Preston – Discover

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Non-human microbiome digest, October 27, 2014

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 8, 2014

Blogging from our yearly retreat in Santa Cruz, California: Rethinking Enterotypes, Wolbachia phylogenomics,  hydrothermal vents, and the influence of salamanders on soil microbiome.

Human Microbiome General

Genes & cells: Body microbes make useful molecules: Human microbiome produces thousands of drug candidates – Tina Hesman Saey – Science News

Human Gut Microbiome

Rethinking “Enterotypes” – Dan Knights – Cell Host and Microbe

“However, as discussed here, several different methods of collapsing enterotype variation into a few discrete clusters suggest that enterotype distribution is continuous and can vary widely within an individual.”

Fecal Bacterial Community Changes Associated with Isoflavone Metabolites in Postmenopausal Women after Soy Bar Consumption – Cindy H. Nakatsu – PLOS ONE

“Using DGGE profiles of PCR amplified 16S rRNA genes (V3 region) to compare microbial communities in fecal samples collected one week before and one week during soy supplementation revealed significant differences (ANOSIM p<0.03) before and after soy supplementation in all subjects. “

Insect microbiome

Phylogenomic analyses uncover origin and spread of the Wolbachia pandemic – Michael Gerth  – Nature Communications

“Here we present the first comprehensive phylogenomic analysis of Wolbachia supergroup relationships based on new whole-genome-shotgun data.”

Coral microbiome

Comparing Bacterial Community Composition of Healthy and Dark Spot-Affected Siderastrea siderea in Florida and the Caribbean – Christina A. Kellogg – PLOS ONE

“Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. “

Soil Microbiome

Summer temperature increase has distinct effects on the ectomycorrhizal fungal communities of moist tussock and dry tundra in Arctic Alaska – Luis N. Morgado – Global Change Biology

“We used Ion Torrent sequencing of the rDNA internal transcribed spacer 2 (ITS2) region to compare ECM fungal communities in plots with and without long-term experimental warming in both dry and moist tussock tundra.”

A metagenomics-based approach to the top-down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest – Donald M. Walker – Ecology and Evolution

“From each sample, DNA was extracted, fungal-specific amplification performed, and 454 pyrosequencing was used to sequence the nuclear ribosomal internal transcribed spacer (ITS2) region and partial ribosomal large subunit (LSU).”

Water microbiome

Evolutionary Strategies of Viruses, Bacteria and Archaea in Hydrothermal Vent Ecosystems Revealed through Metagenomics – Rika E Anderson – PLOS ONE

“Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, “

Metabolomics

Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine – Brianna B. Williams – -Cell Host and Microbe

“Using a combination of genetics, biochemistry, and crystallography, we identify and characterize two phylogenetically distinct enzymes found in the human microbiome that decarboxylate tryptophan to form the β-arylamine neurotransmitter

Techniques

Selective Microbial Genomic DNA Isolation Using Restriction Endonucleases – Helen E. Barnes – PLOS ONE

“Using synthetic genome mixtures, we demonstrate 80% recovery of Escherichia coli genomic DNA even when only femtogram quantities are spiked into 10 µg of human DNA background.”

 More Microbiology

Pseudomonas aeruginosa eradicates Staphylococcus aureus by manipulating the host immunity – Erwan Pernet – Nature Communications

“Our results indicate that a bacterium can eradicate another bacterium by manipulating the host immunity.”

Preparation and evaluation of low-calorie functional ice cream containing inulin, lactulose and Bifidobacterium lactis  – Majid Hashemi- International Journal of Dairy Technology

“This study was aimed to investigate the effects of replacing 5% fat and sugar by inulin and lactulose, respectively, on the survival of Bifidobacterium lactis and physicochemical and sensorial characteristics of the ice cream. “

Microbes in the News

Second Genome, Mayo Clinic team up to explore the microbiome – Stephanie M. Lee – SF Gate

“Second Genome will identify up to eight conditions in which the microbiome potentially plays a role, and the Mayo Clinic will provide human clinical samples for patients with those diseases.”

 Oral health affects overall health – PhillyTrib

“The evidence shows that an infection from periodontitis, or gum disease, can put you at risk for other serious conditions like heart disease, stroke and more.”

Safety Bees: Bacteria From Bees Used To Fight Infections – The Ledger

 “A group of 13 lactic-acid bacteria found in fresh honey from the honey stomach of bees could be the key to bringing an old folk remedy into modern science”

Bik’s Picks  

How dinosaurs divided their meals at the Jurassic dinner table – Science Daily

“How the largest animals to have ever walked on Earth fed, and how this allowed them to live alongside one another in prehistoric ecosystems, is the subject of new research.”

Imitation, Genetic Lineages, and Time Influenced the Morphological Evolution of the Violin – Daniel H. Chitwood – PLOS ONE

“Here, I provide an analysis of morphological evolution in the violin family, sampling the body shapes of over 9,000 instruments over 400 years of history.”

Cat Watch 2014: What’s it like being a cat? – BBC

“Cats are at a crucial point in their evolutionary journey as they transform from solitary hunters to domestic pets, a study by the BBC and the Royal Veterinary College has revealed.”
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Non-human microbiome digest, September 29, 2014

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Microbiome of house mice, rumen, fish species in the same pond, sponges and corals, coastal sediments, and mycobacteria and amoeba in drinking water.

Mammal microbiome

Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high-throughput parallel pyrosequencing – Jakub Kreisinger – Molecular Ecology

“Using 454 pyrosequencing, we performed 16S rDNA GTM barcoding for 30 wild house mice (Mus musculus) and wild-derived inbred strain mice belonging to two subspecies (M. m. musculus and M. m. domesticus)”

Study of methanogen communities associated with different rumen protozoal populations – Alejandro Belanche – FEMS Microbiology Ecology

“Rumen protozoa were harvested from totally faunated sheep, and six protozoal fractions (plus free-living microorganisms) were generated by sequential filtration. “

Microbial profiles of liquid and solid fraction associated biomaterial in buffalo rumen fed green and dry roughage diets by tagged 16S rRNA gene pyrosequencing – K. M. Singh – Molecular Biology Reports

“The rumen bacterial composition of both liquid and solid fraction was surveyed using pyrosequencing of the 16S rRNA gene.”

Bacterial Community Composition and Fermentation Patterns in the Rumen of Sika Deer (Cervus nippon) Fed Three Different Diets – Zhipeng Li – Microbial Ecology

“The present study used 454-pyrosequencing of bacterial 16S ribosomal RNA (rRNA) genes to examine the relationship between rumen bacterial diversity and metabolic phenotypes using three sika deer in a 3 × 3 latin square design.”

Fish microbiome

Do the intestinal microbiotas differ between paddlefish (Polyodon spathala) and bighead carp (Aristichthys nobilis) reared in the same pond? – X.M. Li – Journal of Applied Microbiology

“After 30 days of rearing, the intestinal microbiota of the two fish species was assessed by pyrosequencing of 16S rRNA genes.”

Tending a complex microbiota requires major immune complexity – Keaton Stagaman – Molecular Ecology

“In this issue of Molecular Ecology, Bolnick et al. (2014a) sample the gut microbial community from 150 genetically diverse stickleback isolated from a single lake”

Insect microbiome

The bacterial microbiota of Stolotermes ruficeps (Stolotermitidae), a phylogenetically basal termite endemic to New Zealand – Nicola M. Reid – FEMS Microbiology Ecology

“We identified core bacterial taxa involved in gut processes through combined DNA- and RNA (cDNA)-based pyrosequencing analysis of the 16S nucleotide sequence from five S. ruficeps colonies.”

Genetic groups and endosymbiotic microbiota of the Bemisia tabaci species complex in Japanese agricultural sites – A. Fujiwara – Journal of Applied Entomology

“Use of the cleaved amplified polymorphic sequence technique and mitochondrial cytochrome oxidase subunit I gene sequencing detected five genetic groups”

Sponge and Coral microbiome

Phylogenetic signal in the community structure of host-specific microbiomes of tropical marine sponges – Cole G. Easson and Robert W. Thacker – Frontiers in Microbiology

“As part of the Earth Microbiome Project, we surveyed the microbiomes associated with 20 species of tropical marine sponges collected over a narrow geographic range.”

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

“Using an amplicon pyrosequencing approach, the diversity of both nitrogen-fixing bacteria and of bacterial communities overall was assessed through analysis of nifH and 16S rRNA genes, respectively. “

Biogeography rather than association with cyanobacteria structures symbiotic microbial communities in the marine sponge Petrosia ficiformis  – Ilia Burgsdorf – Forntiers in Microbiology

“16S rRNA gene tag pyrosequencing data of the microbial communities revealed that Chloroflexi, Gammaproteobacteria and Acidobacteria dominated the bacterial communities of all sponges analyzed. “

Soil and sediments microbiome

Interactive effects of C, N and P fertilization on soil microbial community structure and function in an Amazonian rain forest – Nicolas Fanin – Functional Ecology

“Changes in microbial community structure did not affect rates of general processes such as glucose mineralization and cellulose paper decomposition. “

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 .. were compared by shotgun metaproteogenomics.”

Effect of plankton-derived organic matter on the microbial community of coastal marine sediments – Paula Carpintero de Moraes – Journal of Experimental Marine Biology and Ecology

“Analyses of molecular fingerprints of bacterial communities by denaturing gel gradient electrophoresis (DGGE) showed differences in bacterial community composition between both treatments and control just after algae addition. “

Rapid bacterial colonization of low-density polyethylene microplastics in coastal sediment microcosms – Jesse P Harrison – BMC Microbiology

“Sequencing of cloned 16S rRNA genes demonstrated that these communities were dominated after 14 days by the genera Arcobacter and Colwellia “

Water microbiome

Picky, hungry eaters in the cold: persistent substrate selectivity among polar pelagic microbial communities – Andrew D. Steen and Carol Arnosti – Frontiers in Microbiology

“The purpose of this study was to investigate potential factors preventing hydrolysis of pullulan in Svalbard fjord waters. “

Saltwater intrusion history shapes the response of bacterial communities upon rehydration – Tiffanie M. Nelson – Science of The Total Environment

“Bacterial community composition before and after treatment were measured using next generation sequencing of bacterial DNA. “

Diversity of marine microbes in a changing Mediterranean Sea – Gian Marco Luna – Rendiconti Lincei

“This review aims at summarizing the knowledge on microbial diversity in the basin, by focusing on prokaryotes (bacteria and archaea) in pelagic and benthic habitats. “

First evidence of amoebae – mycobacteria association in drinking water network – Vincent Delafont – Environmental Science & Technology

“Direct Sanger sequencing as well as pyrosequencing of environmental isolates demonstrated the frequent association of mycobacteria and FLA”

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Microbiome Digest, August 29, 2014

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

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

Human gut microbiome

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

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

 

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

 

Mammal microbiome

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

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

 

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

 

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

 

Sponges and corals

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

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

Rocks and Water Microbiome

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

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

Food microbiome

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

Bioinformatics

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

Metabolomics

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

Phages and Viruses

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

Microbes in the news

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

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

Bik’s Picks

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

Zombie Bacteria Invasion? Nothing To Worry About – Science 2.0

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

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Non-human microbiome, August 25, 2014

Microbiotas of pigs, two fish species in the same pond, coral-algal associations, hypersaline soil, and marine eukaryotes.

Mammal microbiome

The influence of host’s genetics on the gut microbiota composition in pigs and its links with immunity traits – J. Estellé – Proceedings, 10th World Congress of Genetics Applied to Livestock Production

“A cohort of 60-days old piglets was assessed for fecal microbiota composition by pyrosequencing of the 16S rDNA. “

Fish microbiome

* Do the intestinal microbiotas differ between paddlefish (Polyodon spathala) and bighead carp (Aristichthys nobilis) reared in the same pond? – Xuemei Li – Journal of Applied Microbiology

“After 30-days of rearing the intestinal microbiota of the two fish species were assessed by pyrosequencing of 16S rRNA genes”

Insect microbiome

Microbial Associates of the Vine Mealybug Planococcus ficus (Hemiptera: Pseudococcidae) under Different Rearing Conditions – Lilach Iasur-Kruh – Microbial Ecology

“To examine the possible role of microbial symbionts in virus transmission, the archaeal, bacterial, and fungal microbiota of field and laboratory P. ficus were characterized using molecular and classical microbiological methods. “

Coral microbiome

* The extended phenotypes of marine symbioses: ecological and evolutionary consequences of intraspecific genetic diversity in coral–algal associations – John E. Parkinson and Iliana B. Baums – Frontiers in Microbiology

“Here, we hypothesize that unique combinations of coral and algal individuals yield functional diversity that affects not only the ecology and evolution of the coral holobiont, but associated communities as well. “

Soil microbiome

Salinity-induced differences in soil microbial communities around the hypersaline Lake Urmia – Mohsen Barin – Soil Research

“We tested the hypotheses that salinity reduces microbial biomasses and change the structure of the microbial community.”

Water microbiome

Microbial Community Response to Chlorine Conversion in a Chloraminated Drinking Water Distribution System – Hong Wang – Environmental Science & Technology

“Although high throughput sequencing of 16S rRNA genes revealed a distinct community shift and higher diversity index during the chlorine burn, it steadily returned towards a condition more similar to pre-burn than burn stage.”

Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes – Vera G. Fonseca – Global Ecology and Biogeography

“Here, we ask: (1) if the macroecology of meiobenthic communities is explained mainly by dispersal constraints or by environmental conditions; and (2) if levels of meiofaunal diversity surpass existing estimates based on morphological taxonomy.”

Microbiology of the Built Environment

* A disturbing trend – casual and reckless use of antimicrobial agents in building materials – Jonathan Eisen – MicroBEnet

“So they put in flooring that apparently was impregnated with some sort of antibacterial agent and they have no evidence that it works. “

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